Added exported INDRA evidence-source lists

[tonywu1999]

Summary

• Exported INDRA_DATABASE_SOURCES (22 curated databases) and INDRA_TEXT_MINED_SOURCES (11 text-mining systems), documented on ?indra_evidence_sources. get_network(indra, entities, evidence_sources = INDRA_DATABASE_SOURCES) keeps only edges with curated-database evidence.
• The lists use INDRA's internal names (psp, pc, pe, vhn, bel_lc), from db_sources / reader_sources in indra.util.statement_presentation (INDRA 1.23.0), the module INDRA CoGEx uses. These are the keys CoGEx returns in source_counts; the SOURCE_INFO names (phosphosite, biopax, ...) never appear there, so filtering on them would silently drop PhosphoSitePlus and Pathway Commons evidence.
• backend_capabilities(indra_backend())$evidence_sources returns list(database =, text_mined =).
• A source name in neither list warns rather than errors (INDRA adds sources between releases), suggesting the internal name where there is one, e.g. Use "psp" for "phosphosite". This also applies to getSubnetworkFromIndra(sources_filter =).
• expect_backend_contract() checks the shape of evidence_sources when a backend reports it.

Phase 5b of the API refactor. No new dependencies.

Test plan

• devtools::test(): 1082 pass, 0 fail
• devtools::check(): 0 errors, 0 warnings, 1 pre-existing NOTE (MSstats in Depends not imported)
• New tests: the lists don't overlap and cover every source in indraResponse.rds; capabilities; filtering by each list; warning with the alias hint and for an unknown name
• Live CoGEx query (1926 statements): every source_counts key is in the two lists
• ?indra_evidence_sources example against live INDRA: 31 edges, 16 with database evidence, 19 with text-mined evidence

Co-Authored-By: Claude noreply@anthropic.com

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📥 Commits

Reviewing files that changed from the base of the PR and between 619c4fc and c212f46.

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📒 Files selected for processing (11)

• NAMESPACE
• NEWS.md
• R/AllGenerics.R
• R/backend-indra.R
• R/getSubnetworkFromIndra.R
• man/backend_capabilities.Rd
• man/getSubnetworkFromIndra.Rd
• man/get_network.Rd
• man/indra_evidence_sources.Rd
• tests/testthat/helper-contract.R
• tests/testthat/test-backend-indra.R

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 87.07%. Comparing base (619c4fc) to head (c212f46).

Additional details and impacted files

@@            Coverage Diff             @@
##            devel     #131      +/-   ##
==========================================
+ Coverage   86.97%   87.07%   +0.09%     
==========================================
  Files          24       24              
  Lines        2757     2778      +21     
==========================================
+ Hits         2398     2419      +21     
  Misses        359      359              

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